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assignpKasToSpecies(mets, neutralMolfileDir, msDistrDir, pKaDir)

Use each metabolite’s InChI and ChemAxon’s cxcalc (calculator plugin) to get pKas(I=0), charges and numbers of protons for all microspecies present at pH 5-9.

[speciespKas,includedMets] = assignpKasToSpecies(mets,neutralMolfileDir,msDistrDir,pKaDir)

INPUTS mets Cell array of metabolite ID. Current implementation

assumes ID are formatted as BiGG_ID[Compartment]; e.g., atp[c] for ATP in cytosol.

neutralMolfileDir Path to directory containing molfiles for neutral

metabolites. Molfiles must be named with the metabolite ID in mets; e.g., atp.mol.

msDistrDir Path to directory containing metabolite species

distributions at pH 5, 6, 7, 8 and 9. Species distributions are created with the ChemAxon calculator plugin. Names of SD files containing species distributions should be formatted as metID_msdistr_pHA.sdf; e.g., atp_msdistr_pH5.sdf.

pKaDir Path to directory containing pKa estimates for

metabolites. pKas are estimated with the ChemAxon calculator plugin. Names of text files containing pKa estimates should be formatted as metID_pkas.txt; e.g., atp_pkas.txt.

OUTPUTS speciespKas Structure containing the following fields for each

metabolite:

.inchis n x 1 cell array with a species-specific InChI string

for each species. inchis(1) = InChI for species 1 etc. NOTE: Species 1 is the species with the fewest hydrogen atoms etc.

.formulas n x 1 cell array with species-specific chemical

formulas.

.zs n x 1 vector containing the charge on each species. .nHs n x 1 vector containing the number of hydrogen atoms in

each species.

.majorMSpH7 n x 1 boolean vector with a logical 1 in the row for

the major microspecies at pH 7 according to ChemAxon.

.abundanceAtpH7 n x 1 vector with species percentage abundance at pH 7. .pKas n x n matrix where element i,j is the pKa for the

acid-base equilibrium between species i and j.

includedMets Cell array of metabolite ID for those metabolites that

were included in speciespKas. Should include all metabolites that had molfiles in neutralMolfileDir.

estimate_pKa(mets, inchi, npKas, takeMajorTaut)

Estimates pKa values with ChemAxon’s Calculator plugins and determines all physiologically relevant pseudoisomers.

pseudoisomers = estimate_pKa(mets,inchi,npKas,takeMajorTaut)

INPUTS mets m x 1 array of metabolite identifiers. inchi m x 1 array of InChI strings for metabolites in mets.

OPTIONAL INPUTS npKas Maximum number of acidic and basic pKa values to

estimate for each metabolite. Default is 20.

takeMajorTaut {1, (0)}. If 1, pKa values are estimated for the major

tautomer at pH 7. If 0 (default), they are estimated for the given tautomer.

OUTPUTS pseudoisomers m x 1 structure array where each element has the fields

listed below. All fields are empty for metabolites where no InChI is given. Fields:

.success Logical one (true) for metabolites where an InChI was

given.

.met Metabolite identifier from mets without compartment

abbreviation.

.pKas p x p matrix where element (i,j) is the pKa value for

the acid-base equilibrium between pseudoisomers i and j.

.zs p x 1 array of pseudoisomer charges. .nHs p x 1 array of number of hydrogen atoms in each

pseudoisomer’s chemical formula.

.majorMSpH7 p x 1 logical array. True for the most abundant

pseudoisomer at pH 7.

REQUIRES cxcalc ChemAxon’s Calculator plugin, with licence cxcalc is part of Marvin Beans, available by academic licence from ChemAxon https://www.chemaxon.com/download/marvin-suite/#mbeans https://docs.chemaxon.com/display/docs/Installation+MS#InstallationMS-MarvinBeansforJava https://docs.chemaxon.com/display/CALCPLUGS/cxcalc+command+line+tool https://docs.chemaxon.com/display/docs/Installation+MS#InstallationMS-Linux/SolarisLinux/Solaris